Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(biomaRt)
library(fgsea)
library(goseq)

theme_set(theme_classic())
graph_weight = params$graph_weight
graph_weight
## [1] "2.0"

Check enrichment of gene sets

Read in gene info and gene set assignments

cell_type_name = "CD8T"
file_tag = sprintf("%s_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   23.00   24.00   25.00   24.55   25.00   26.00
length(n_genes)
## [1] 40
sort(n_genes)
##  [1] 23 23 23 23 23 23 23 23 23 24 24 24 24 24 24 24 24 24 25 25 25 25 25 25 25
## [26] 25 25 25 25 25 25 26 26 26 26 26 26 26 26 26
sum(n_genes)
## [1] 982

Find gene symbols

Find gene symbols from bioMart.

All the gene symbols that can be found in bioMart are consistent with what we have. So no need to run it.

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"), 
                filters = "external_gene_name", 
                values = assayed_genes, 
                mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]

table(assayed_genes %in% gene_BM$external_gene_name)

t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]

table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}
## [1] "C7orf55"
## [1] "FMC1-LUC7L2" "FMC1"       
## [1] "MARS"
## [1] "MARS1" "SLA2" 
## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "APITD1"
## [1] "CENPS-CORT" "CENPS"     
## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"
table(is.na(a2s))
## 
## FALSE  TRUE 
##  1120   139
table(a2s == assayed_genes, useNA = 'ifany')
## 
## FALSE  TRUE  <NA> 
##    71  1049   139
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]
##      sym_in_data   sym_limma
##  1:        ZNRD1      POLR1H
##  2:      C2orf43        LDAH
##  3:       FAM45A     DENND10
##  4:        MTERF      MTERF1
##  5:        NARG2        ICE2
##  6:     C6orf203      MTRES1
##  7:       HRSP12        RIDA
##  8:        FOPNL       CEP20
##  9:         WARS       WARS1
## 10:         LINS       LINS1
## 11:       RRNAD1    METTL25B
## 12:      FAM122B      PABIR2
## 13:       WDYHV1       NTAQ1
## 14:    HIST1H2BD       H2BC5
## 15:       AGPAT6       GPAT4
## 16:     C1orf123        CZIB
## 17:     KIAA1841       SANBR
## 18:      C2orf44        WDCP
## 19:      TMEM155      SMIM43
## 20:      C7orf55 FMC1-LUC7L2
## 21:      C9orf89      CARD19
## 22:     C11orf82       DDIAS
## 23:     XRCC6BP1       ATP23
## 24:         MARS       MARS1
## 25:     C19orf55     PROSER3
## 26:    HIST1H2AE       H2AC8
## 27:         QARS       EPRS1
## 28:       APITD1  CENPS-CORT
## 29:      CCDC101       SGF29
## 30:        PDDC1       GATD1
## 31:      EFCAB4A     CRACR2B
## 32:      EIF2S3L     EIF2S3B
## 33:    HIST1H2BC       H2BC5
## 34:          WRB        GET1
## 35:     TMEM194B       NEMP2
## 36:     HIST1H4C        H4C3
## 37:     HIST1H4J       H4C11
## 38:       ZNF720      KRBOX5
## 39:    HIST1H2BH       H2BC9
## 40:       FAM49A       CYRIA
## 41:        TTC37       SKIC3
## 42:      C1orf85        GLMP
## 43:     C9orf114      SPOUT1
## 44:   HIST2H2AA4      H2AC19
## 45:    HIST2H2BF      H2BC18
## 46:    C10orf128     TMEM273
## 47:     TCTEX1D2     DYNLT2B
## 48:     C17orf89     NDUFAF8
## 49:        PHBP3      PHB1P3
## 50:      SEPT7P7   SEPTIN7P7
## 51:    LINC00493      SMIM26
## 52:    HIST1H2BN      H2BC15
## 53:       ATP5J2      ATP5MF
## 54:        AKAP2  PALM2AKAP2
## 55:        WDR65      CFAP57
## 56:    SRP14-AS1    SRP14-DT
## 57: CTC-436P18.1  SMIM15-AS1
## 58:     HIST1H3G        H3C8
## 59:     EFTUD1P1      EFL1P1
## 60:     ATP5A1P3   ATP5F1AP3
## 61:     CCDC109B        MCUB
## 62:      C1orf63       RSRP1
## 63:       TMEM66       SARAF
## 64:       PCNXL2       PCNX2
## 65:         ACRC        GCNA
## 66:       AMICA1        JAML
## 67:       PRMT10       PRMT9
## 68:      FAM102A       EEIG1
## 69:         SELM     SELENOM
## 70:       NBPF16      NBPF15
## 71:       RPL9P9      RPL9P8
##      sym_in_data   sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma), gene_symbol := sym_limma]

dim(gene_info)
## [1] 1259    3
gene_info[1:5,]
##    sym_in_data sym_limma gene_symbol
## 1:    C1orf112  C1orf112    C1orf112
## 2:      MAD1L1    MAD1L1      MAD1L1
## 3:        ICA1      ICA1        ICA1
## 4:     NDUFAF7   NDUFAF7     NDUFAF7
## 5:         ST7       ST7         ST7
t1 = table(gene_info$gene_symbol)
table(t1)
## t1
##    1    2 
## 1255    2
gene_info[gene_symbol %in% names(t1)[t1 == 2],]
##    sym_in_data sym_limma gene_symbol
## 1:   HIST1H2BD     H2BC5       H2BC5
## 2:   HIST1H2BC     H2BC5       H2BC5
## 3:      RPL9P8    RPL9P8      RPL9P8
## 4:      RPL9P9    RPL9P8      RPL9P8
gene_info[sym_in_data == "HIST1H2BC", gene_symbol:="H2BC4"]
gene_info[sym_in_data == "RPL9P9", gene_symbol:="RPL9P9"]

Prepare gene set information

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]]    = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
gmtfile[["immune"]]   = "../Annotation/c7.all.v2023.2.Hs.symbols.gmt"

pathways = list()
for(k1 in names(gmtfile)){
  pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}

names(pathways)
## [1] "reactome" "go_bp"    "immune"
sapply(pathways, length)
## reactome    go_bp   immune 
##     1692     7647     5219

Filter gene sets for size between 10 and 500.

lapply(pathways, function(v){
  quantile(sapply(v, length), probs = seq(0, 1, 0.1), na.rm = TRUE)
})
## $reactome
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    7.0    9.0   12.0   17.0   23.0   31.0   44.0   71.8  120.9 1463.0 
## 
## $go_bp
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    6.0    8.0   10.0   14.0   19.0   29.0   46.0   80.8  183.0 1966.0 
## 
## $immune
##   0%  10%  20%  30%  40%  50%  60%  70%  80%  90% 100% 
##    5  162  193  197  199  199  200  200  200  200 1992
for(k1 in names(pathways)){
  p1 = pathways[[k1]]
  pathways[[k1]] = p1[sapply(p1, length) %in% 10:500]
}

Conduct enrichment analysis

dim(gene_info)
## [1] 1259    3
gene_info[1:2,]
##    sym_in_data sym_limma gene_symbol
## 1:    C1orf112  C1orf112    C1orf112
## 2:      MAD1L1    MAD1L1      MAD1L1
max_n2kp = 10

goseq_res = NULL

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info$sym_in_data %in% gene_sets[[k]]
  names(genes) = gene_info$gene_symbol
  table(genes)
  
  pwf = nullp(genes, "hg38", "geneSymbol")
  
  for(k1 in names(pathways)){
    p1 = pathways[[k1]]
    res1 = goseq(pwf, "hg38", "geneSymbol", 
                 gene2cat=goseq:::reversemapping(p1))
    res1$FDR  = p.adjust(res1$over_represented_pvalue, method="BH")
    
    nD = sum(res1$FDR < 0.05)
    
    if(nD > 0){
      res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
      res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
      res1$category = gsub("_", " ", res1$category)
      res1$category = tolower(res1$category)
      res1$category = substr(res1$category, start=1, stop=120)
      goseq_res[[set_k]][[k1]] = res1
    }
  }
}
## [1] 1
##  [1] "MTIF2"    "KHSRP"    "MRPS33"   "NDUFAF5"  "CDK5RAP1" "EARS2"   
##  [7] "MTFMT"    "SARS2"    "GTPBP10"  "DHX58"    "ATPAF1"   "NDUFAF4" 
## [13] "C6orf203" "MTO1"     "MRRF"     "MALSU1"   "MRPL55"   "NDUFS4"  
## [19] "PHAX"     "MRPL48"   "ZNF431"   "MRPL23"   "CCDC109B"

## [1] 2
##  [1] "CENPQ"   "CENPO"   "ZNF816"  "RPS17"   "TNF"     "APBA2"   "RPL34"  
##  [8] "RPS12"   "RASGRF2" "EGR1"    "RPL21"   "FOSB"    "JUND"    "SORL1"  
## [15] "RPS27A"  "RPL9"    "RBKS"    "JUNB"    "RPLP2"   "RPS27"   "DNHD1"  
## [22] "RPS23"   "RPS18"

## [1] 3
##  [1] "MAD1L1"   "SLC25A14" "ERCC2"    "IMPDH1"   "C17orf75" "GTF2H3"  
##  [7] "CDC20"    "DCAF4"    "CKS2"     "MCEE"     "UROD"     "PDZD2"   
## [13] "CCNB1"    "CDK7"     "COPS3"    "CCNB2"    "MTHFD2L"  "POLE"    
## [19] "BTLA"     "HIST1H4J" "PRIM1"    "C1orf85"  "STK19"    "MUC20"

## [1] 4
##  [1] "DERL2"     "SMUG1"     "GLUL"      "TMOD3"     "LINS"      "PLIN2"    
##  [7] "MZT2B"     "HIST1H2BD" "GLB1"      "KBTBD2"    "IFRD2"     "C17orf89" 
## [13] "PPIL3"     "IFRD1"     "PIK3IP1"   "YPEL5"     "BTG1"      "SLC38A2"  
## [19] "SKIL"      "PDCD4"     "FAM102A"   "PFKFB3"    "RALGAPA1"

## [1] 5
##  [1] "TBPL1"         "NT5C2"         "WDR13"         "IFI6"         
##  [5] "XAF1"          "TMEM241"       "APH1B"         "WARS"         
##  [9] "GTF2A2"        "TATDN1"        "LZTFL1"        "TRIM68"       
## [13] "GTSF1"         "FCRL6"         "PSMG1"         "UBXN2B"       
## [17] "TSTD1"         "TRGC2"         "PATL2"         "TRGV2"        
## [21] "AC092580.4"    "RP11-552M11.4" "HMGB1P24"      "AC139149.1"   
## [25] "CTD-3214H19.4"

## [1] 6
##  [1] "MFAP3"    "FAR2"     "CAPN15"   "PIEZO1"   "POP4"     "CD86"    
##  [7] "CD160"    "DHDDS"    "NPC2"     "IFIT3"    "IFIT2"    "NME2P1"  
## [13] "L3HYPDH"  "HRSP12"   "PRMT7"    "DPH6"     "C1orf123" "CTLA4"   
## [19] "POP5"     "IFIT1"    "TMEM120A" "POTEKP"   "PVT1"

## [1] 7
##  [1] "KHDC1"         "ABHD16B"       "ZNF93"         "NPM1P33"      
##  [5] "RP11-247I13.3" "RP11-270C12.3" "PGAM4"         "PIN4P1"       
##  [9] "RP11-247I13.6" "SEPT7P7"       "PA2G4P4"       "RP11-782C8.1" 
## [13] "BTF3P10"       "RPS27AP2"      "AC007041.2"    "RPS19P3"      
## [17] "RN7SL56P"      "GAPDHP60"      "RNF138P1"      "KB-1507C5.2"  
## [21] "SLC2A3P4"      "HSPA8P5"       "ANP32AP1"      "CTB-52I2.4"   
## [25] "CTD-2545M3.2"  "RP4-739H11.4"

## [1] 8
##  [1] "MAP4K5"        "KIF4A"         "SPTLC2"        "RAD51C"       
##  [5] "MCM9"          "SMC4"          "CACYBP"        "AKR1A1"       
##  [9] "CCR2"          "TEP1"          "NPHP4"         "SLC2A8"       
## [13] "HIRIP3"        "RNF207"        "LRRC28"        "PLA2G6"       
## [17] "EFCAB7"        "HSPA1B"        "TRAV21"        "NAP1L1P3"     
## [21] "RP11-773D16.1" "RP11-307P22.1" "CTD-2521M24.9" "C1orf63"      
## [25] "RP11-727F15.9"

## [1] 9
##  [1] "VPS41"    "SH3BP2"   "DEPDC5"   "ARHGEF18" "LIG1"     "DDX49"   
##  [7] "BRD8"     "NPRL2"    "CHTF18"   "TPGS2"    "ACTL6A"   "MTF2"    
## [13] "SUV39H2"  "FARP1"    "CXXC1"    "TAF10"    "TRAPPC11" "RMDN1"   
## [19] "TECPR1"   "SSH2"     "PIP4K2A"  "BRD2"     "PPP1R10"

## [1] 10
##  [1] "PTPN18"        "MAP3K13"       "ZNF684"        "TXNDC17"      
##  [5] "PUS7L"         "TROAP"         "GEMIN6"        "MPPE1"        
##  [9] "KIAA1841"      "CTSB"          "C11orf82"      "TBCA"         
## [13] "ZBED2"         "GEN1"          "TMEM194B"      "RP11-64B16.2" 
## [17] "NCKIPSD"       "AC098614.2"    "RPF2P1"        "CCT8P1"       
## [21] "BDH2P1"        "GAPDHP2"       "RP11-844P9.3"  "PAICSP4"      
## [25] "RP11-473N11.2"

## [1] 11
##  [1] "CD84"           "ZNF85"          "GALK1"          "MS4A6A"        
##  [5] "STK25"          "CCRL2"          "STYXL1"         "NARG2"         
##  [9] "TMEM138"        "ZBTB39"         "ZNF613"         "SPATA13"       
## [13] "CCDC30"         "RP11-12M9.4"    "HNRNPKP2"       "RP3-342P20.2"  
## [17] "PA2G4P2"        "AC002331.1"     "HNRNPA1P55"     "CCL3L3"        
## [21] "RBBP4P5"        "HMGB1P8"        "HNRNPA1P16"     "CTB-31O20.3"   
## [25] "RP11-686D22.10"

## [1] 12
##  [1] "TM7SF3"       "TIPIN"        "TIMM9"        "PLA2G15"      "GABPB1"      
##  [6] "DOT1L"        "ZNF419"       "DUS4L"        "LOXL3"        "FANCL"       
## [11] "TIMM10"       "RNF121"       "CCDC28B"      "RNF25"        "PRIMPOL"     
## [16] "CDCA7L"       "SESTD1"       "TDRD7"        "GM2A"         "CHAMP1"      
## [21] "FANCG"        "GK3P"         "RP11-402J6.3" "ATP5A1P3"

## [1] 13
##  [1] "PIM2"         "HAVCR1"       "PECR"         "USF1"         "FCRL3"       
##  [6] "WDR41"        "NAALADL1"     "AC004840.9"   "COA3"         "CMC1"        
## [11] "CCL3L1"       "RAB12"        "TRAV24"       "RP11-2F9.3"   "MIR29B1"     
## [16] "PET100"       "RP11-693N9.2" "LINC00426"    "RN7SL749P"    "AC005329.7"  
## [21] "AP000462.1"   "SNORD3A"      "C9orf72"      "MS4A1"

## [1] 14
##  [1] "DYRK4"         "GLT8D1"        "ID3"           "MFSD9"        
##  [5] "TMEM19"        "NTAN1"         "TMSB15B"       "ZNF511"       
##  [9] "RP13-383K5.4"  "CD27-AS1"      "UBA52P6"       "ACTBP8"       
## [13] "RPL19P12"      "ARPC3P1"       "PHBP3"         "ATF4P3"       
## [17] "TCP1P1"        "TPI1P2"        "ETF1P2"        "RPL13P5"      
## [21] "RPL37P23"      "GAPDHP38"      "RP11-382J24.2" "PSMC1P9"      
## [25] "MIR3661"       "AC024592.12"

## [1] 15
##  [1] "NOP16"       "NTHL1"       "WDR7"        "THOC5"       "FAHD2A"     
##  [6] "NENF"        "METTL8"      "EMG1"        "IMP4"        "C19orf47"   
## [11] "WDR43"       "ZFP62"       "ZNF770"      "ZBTB48"      "UAP1"       
## [16] "SGSM2"       "RPL32"       "EPB41"       "CXCR5"       "ZNF589"     
## [21] "RPS26"       "SELM"        "RP11-51J9.5"

## [1] 16
##  [1] "REC8"           "DHRS12"         "GDAP1"          "PRR4"          
##  [5] "SCPEP1"         "ORMDL2"         "RRM2"           "MZT2A"         
##  [9] "ASB8"           "HIST1H4C"       "SLC26A6"        "RP11-386G11.10"
## [13] "RGCC"           "CPQ"            "FOXP1"          "PMEPA1"        
## [17] "FAM117B"        "NPAT"           "TC2N"           "GPR183"        
## [21] "PLK3"           "GOLGA8A"        "SATB1"          "TSC22D2"

## [1] 17
##  [1] "NDUFAF7" "NSMAF"   "IL4R"    "USP48"   "UTP6"    "PTP4A1"  "MYB"    
##  [8] "PGPEP1"  "PPCDC"   "NARF"    "PMAIP1"  "PPOX"    "SEC24D"  "FCGR3B" 
## [15] "FBXO22"  "ZNF232"  "GNG4"    "BOLA1"   "CAPN12"  "FCGR3A"  "LEF1"   
## [22] "GNAQ"    "DHRS3"   "NR1D2"

## [1] 18
##  [1] "DUSP12"   "AAAS"     "DHPS"     "NUP107"   "GALE"     "NUP85"   
##  [7] "COQ3"     "FHOD1"    "ASNSD1"   "UCK2"     "LPP"      "CETN3"   
## [13] "VPS37A"   "GALK2"    "AGPAT6"   "NFU1"     "TMEM126A" "CTDNEP1" 
## [19] "UCKL1"    "ATP5J2"   "ABHD14A"  "GGT7"     "OBSCN"

## [1] 19
##  [1] "RP3-324O17.4"     "MDGA1"            "PDE6B"            "SLC35A5"         
##  [5] "GSTM4"            "LRTOMT"           "MYL5"             "XXbac-B562F10.11"
##  [9] "GS1-124K5.2"      "GYG1P3"           "AC115617.2"       "GOT2P3"          
## [13] "CTD-2301A4.3"     "ACRC"             "POU6F1"           "TCEAL3"          
## [17] "RP11-91K8.4"      "ACTBP12"          "RP1-187B23.1"     "AP001468.1"      
## [21] "ATP1B3-AS1"       "RP11-44N11.1"     "TMEM9B-AS1"       "LINC00944"       
## [25] "RP11-320M16.1"    "CTD-2017D11.1"

## [1] 20
##  [1] "TMEM134"       "ZBTB8OS"       "C2orf76"       "RPSAP47"      
##  [5] "ZNF28"         "TRGV10"        "RPSAP54"       "RP4-694B14.5" 
##  [9] "KANSL1-AS1"    "RNU2-63P"      "NPM1P19"       "RP11-350G8.3" 
## [13] "SAPCD1"        "RP11-567G24.1" "AC093391.2"    "EEF1A1P14"    
## [17] "CDC42P1"       "FAM200B"       "AC018462.3"    "EEF1A1P10"    
## [21] "CTB-33G10.1"   "TPM3P6"        "RP11-1012A1.7" "RP13-638C3.4" 
## [25] "RP11-209D14.4" "ACTBP9"

## [1] 21
##  [1] "ICA1"       "GBA2"       "REXO1"      "RABGGTA"    "ILVBL"     
##  [6] "SRM"        "PARP2"      "FGFBP2"     "MMS22L"     "SPON2"     
## [11] "COG5"       "XRCC6BP1"   "NT5DC1"     "HIST1H2BC"  "ZNF765"    
## [16] "HIST2H2AA4" "HIST2H2BF"  "TRAV14DV4"  "LINC00493"  "CNOT7P1"   
## [21] "HIST1H2BN"  "AC004069.2" "HIST1H3G"   "HNRNPA1P50" "FRMD4A"

## [1] 22
##  [1] "C1orf112" "AGA"      "RNF13"    "P2RX5"    "GSR"      "TYK2"    
##  [7] "GOSR2"    "FIGNL1"   "IDH1"     "TAMM41"   "TOMM40L"  "B2M"     
## [13] "AFMID"    "KNTC1"    "ENTPD5"   "TMSB4X"   "TREX1"    "RGPD5"   
## [19] "DKK3"     "PPP2R5C"  "STK17B"   "EPHA1"    "NELL2"    "MALAT1"

## [1] 23
##  [1] "ZNF268"        "RRNAD1"        "THAP2"         "SNHG11"       
##  [5] "EIF2S3L"       "CATSPER2P1"    "TRAV35"        "RP11-383G10.3"
##  [9] "CALM2P3"       "RPS12P26"      "AC090804.1"    "SKP1P1"       
## [13] "RPS11P5"       "CTC-338M12.4"  "MAPKAPK5-AS1"  "RP11-446E9.1" 
## [17] "RP11-32B5.1"   "AP000476.1"    "FAM21FP"       "RP11-394D2.1" 
## [21] "RBBP4P1"       "RP11-638I2.10" "CTD-2022H16.3" "RP11-304L19.5"
## [25] "RP11-265N6.3"  "AC006129.4"

## [1] 24
##  [1] "MED24"         "ZNRD1"         "POLR2I"        "NSMCE4A"      
##  [5] "EPAS1"         "UXT"           "SLC41A2"       "CLSTN3"       
##  [9] "TBCD"          "MFSD6"         "PPP4R1"        "ALG8"         
## [13] "MED11"         "POLR2H"        "IL15"          "MEI1"         
## [17] "LCORL"         "TMEM107"       "PPARA"         "TRGV3"        
## [21] "MRPL33"        "RP11-33B1.1"   "RP11-416A17.6" "MIR3615"      
## [25] "RP11-297D21.4"

## [1] 25
##  [1] "MTHFS"         "DRAM2"         "RHEBL1"        "LRRC45"       
##  [5] "NME6"          "PIGW"          "MT1X"          "ZNF720"       
##  [9] "TRBV4-2"       "TRAV19"        "ANAPC10P1"     "RSC1A1"       
## [13] "RP11-122G18.7" "RP11-350G13.1" "RP11-119F19.2" "NPM1P34"      
## [17] "AC104820.2"    "RP11-262H14.3" "NDUFA9P1"      "RPSAP4"       
## [21] "WDR65"         "RP11-179A18.1" "TRGV7"         "CTB-4E7.1"    
## [25] "AL161784.1"    "RP11-705C15.5"

## [1] 26
##  [1] "TNFRSF9"       "EVC"           "NFE2L1"        "CRTAM"        
##  [5] "C3orf14"       "SMIM19"        "RP11-254B13.4" "BACH2"        
##  [9] "NBPF14"        "NR4A2"         "AMICA1"        "NBPF10"       
## [13] "AC018720.10"   "NAA16"         "CHD2"          "TSHZ2"        
## [17] "TTC3"          "PLGLB1"        "KLHL25"        "NBPF16"       
## [21] "AC084018.1"    "HCG4P5"        "MTND4P12"      "RP11-335G20.7"
## [25] "SLC7A5P1"

## [1] 27
##  [1] "MBNL3"         "FAH"           "SNX8"          "SCRN2"        
##  [5] "FUOM"          "OXSM"          "FAM122B"       "DBF4B"        
##  [9] "DNASE1"        "RP3-395M20.8"  "DBNDD2"        "AP000620.1"   
## [13] "TPMTP1"        "PLXND1"        "AOAH"          "CDC42EP3"     
## [17] "ZMAT1"         "RPS3AP26"      "RP11-572P18.1" "RPL10P3"      
## [21] "RPL9P8"        "RPL3P4"        "RPS3AP6"       "RPL9P9"       
## [25] "RPL9P7"

## [1] 28
##  [1] "EGR2"          "IL10"          "TNFAIP8L2"     "C19orf55"     
##  [5] "CMAHP"         "ARHGAP11B"     "ZNF257"        "AC018804.7"   
##  [9] "AC009403.2"    "LYPLA1P3"      "AC012318.3"    "RP4-742C19.12"
## [13] "ZNF826P"       "AC011747.4"    "ZEB1-AS1"      "RP11-271C24.3"
## [17] "SRP14-AS1"     "GMPSP1"        "RP11-889L3.4"  "MIR146A"      
## [21] "SF3A3P2"       "USP30-AS1"     "TRAV30"        "EFTUD1P1"     
## [25] "RP11-265N6.2"  "RIMKLB"

## [1] 29
##  [1] "RNF10"     "SMG6"      "MICALL1"   "GMPR2"     "CNOT2"     "MTFR1L"   
##  [7] "APTX"      "CASP1"     "HAUS2"     "KSR1"      "MAP3K6"    "LIMD1"    
## [13] "C2orf44"   "DALRD3"    "PCGF5"     "CNOT10"    "EIF4ENIF1" "ZNF544"   
## [19] "TNRC6C"    "TNRC6B"    "CNOT6L"    "BTG2"      "PLA2G4B"

## [1] 30
##  [1] "CHI3L2"         "OCEL1"          "NHP2P1"         "IL18RAP"       
##  [5] "C2orf43"        "FAM45A"         "MTERF"          "DTD2"          
##  [9] "NUDT7"          "C9orf89"        "ADCK5"          "EFCAB4A"       
## [13] "SLC9A9"         "ZNF525"         "TRGV5"          "TRBV9"         
## [17] "TRDV1"          "TRDC"           "RP4-800M22.1"   "RPL19P21"      
## [21] "ADH5P4"         "AC144530.1"     "STARD4-AS1"     "RP11-317N8.4"  
## [25] "RP11-1094M14.7" "RP11-282O18.6"

## [1] 31
##  [1] "Z97634.3"      "RASGRP2"       "TCF7"          "MAN1C1"       
##  [5] "ACVR2A"        "CCR7"          "C1orf162"      "PLAC8"        
##  [9] "LDLRAP1"       "PLXDC1"        "TMEM150A"      "CD248"        
## [13] "YPEL2"         "TRABD2A"       "MIR4461"       "CTD-3092A11.1"
## [17] "RP11-632K20.7" "LTB"           "CHRM3-AS2"     "WHAMMP2"      
## [21] "RP11-747H7.3"  "RP11-1000B6.3" "KCNQ1OT1"      "RP1-313I6.12" 
## [25] "RP11-434H6.7"

## [1] 32
##  [1] "CCL3"     "RABGAP1"  "GNPTAB"   "SLC12A4"  "CCL4"     "GCHFR"   
##  [7] "PRSS23"   "TMPRSS3"  "SLC39A13" "DNAJC18"  "ETFDH"    "METTL18" 
## [13] "ZNF80"    "PDDC1"    "WRB"      "TNFRSF18" "CCL4L2"   "AGER"    
## [19] "MSH5"     "UBE2D3P2" "MIR142"   "PHLDB3"   "PER1"     "CD55"

## [1] 33
##  [1] "CD200"         "C14orf93"      "TFDP2"         "YIPF2"        
##  [5] "NDUFAF6"       "PAQR4"         "TMEM155"       "LAIR2"        
##  [9] "TRANK1"        "ZNF678"        "EDARADD"       "CRYGS"        
## [13] "LINC00484"     "BHLHE40-AS1"   "RP11-305L7.3"  "RP4-728D4.2"  
## [17] "TRAV1-2"       "RP11-493L12.6" "PMF1-BGLAP"    "DGKA"         
## [21] "MAK"           "RP11-514P8.6"  "RPS26P6"       "HLA-W"        
## [25] "RP13-488H8.1"

## [1] 34
##  [1] "POLD3"   "PTPN4"   "UBXN8"   "IFNG"    "RCOR3"   "NR2C1"   "SNX14"  
##  [8] "GPN2"    "FAM50B"  "MITD1"   "PPP1R32" "C7orf55" "ATPAF2"  "CADM1"  
## [15] "SCML1"   "TXK"     "CLDND1"  "ABLIM1"  "SLC38A1" "NEK1"    "FBXO32" 
## [22] "POLR2J3" "LDOC1"   "HLA-J"

## [1] 35
##  [1] "IFI27"         "WDR53"         "ZNF749"        "FAM49A"       
##  [5] "ZNF649"        "CPT1B"         "TRAV8-2"       "TRAV13-1"     
##  [9] "TRAV16"        "TRAV29DV5"     "PDCL3P5"       "NPM1P32"      
## [13] "RP1-102E24.1"  "RPS19P1"       "PSMA6P1"       "PTGES3P2"     
## [17] "RP3-340B19.5"  "PRDX3P1"       "RP11-288E14.2" "RPL7AP31"     
## [21] "RP11-81H14.2"  "MTRNR2L3"      "RP11-511H9.4"  "RPPH1"        
## [25] "AC006483.1"    "LUZP6"

## [1] 36
##  [1] "CDKL1"        "TTLL4"        "MGAT4A"       "HECA"         "RCAN3"       
##  [6] "NR4A3"        "PCNXL2"       "RASGEF1B"     "TIPARP"       "PRMT10"      
## [11] "FILIP1L"      "ZBTB20"       "RGPD6"        "DENND5A"      "ANKRD37"     
## [16] "SELL"         "FAM169A"      "AC021593.1"   "MTND1P23"     "LINC00674"   
## [21] "PSMD6-AS2"    "RP11-285F7.2" "ZNF10"        "QRSL1P3"

## [1] 37
##  [1] "GCFC2"         "OAS1"          "GZMB"          "ENO3"         
##  [5] "NCOA7"         "GBP1"          "MT2A"          "RSAD2"        
##  [9] "SPPL2A"        "IRF8"          "SFR1"          "SLAMF8"       
## [13] "AMDHD2"        "GNGT2"         "KIR3DL1"       "ITGAM"        
## [17] "NINJ2"         "SWI5"          "PRF1"          "RP11-365H23.1"
## [21] "KIR2DS4"       "PTGES3P1"      "AKAP2"         "KIR2DL3"      
## [25] "SERHL2"

## [1] 38
##  [1] "PAFAH1B1"     "LIN7B"        "PON2"         "KLRB1"        "CCDC77"      
##  [6] "ACTR10"       "FOPNL"        "KLRC1"        "AHI1"         "BORA"        
## [11] "CXCL13"       "PANK4"        "MGAT4B"       "SLC38A9"      "CEP57L1"     
## [16] "HLA-DQA1"     "CCL4L1"       "KLRC2"        "METTL6"       "TCTEX1D2"    
## [21] "KIR3DL2"      "RP11-345J4.6" "MPP7"

## [1] 39
##  [1] "TNFSF10"      "PTGER2"       "IFI44L"       "IFI44"        "XCL1"        
##  [6] "XCL2"         "TRPT1"        "CX3CR1"       "MT1E"         "HOPX"        
## [11] "RP11-23P13.6" "ZNF683"       "NAP1L4P1"     "MTHFD2P7"     "EEF1GP1"     
## [16] "C10orf128"    "TRBV20-1"     "RP5-1053E7.3" "RP1-182O16.1" "RNU2-2P"     
## [21] "TSEN15P1"     "SNRPEP4"      "MIR155HG"     "RNU1-125P"    "AL358333.1"

## [1] 40
##  [1] "EVI5"          "WIPI1"         "LTBP4"         "RGS1"         
##  [5] "PMM1"          "FADS2"         "IRF4"          "BCAS3"        
##  [9] "PELP1"         "AMFR"          "CXCR6"         "TRAV12-2"     
## [13] "TMEM66"        "ATXN7"         "NPIPB3"        "EIF1"         
## [17] "NPIPB4"        "GPRASP1"       "KLRK1"         "MTND2P28"     
## [21] "CTD-2328D6.1"  "RPL41"         "NPIPB5"        "MTATP6P1"     
## [25] "CTD-2031P19.4"

for(n1 in names(goseq_res)){
  k = as.numeric(gsub("set_", "", n1))
  print(n1)
  print(gene_sets[[k]])
  print(goseq_res[[n1]])

}
## [1] "set_1"
##  [1] "MTIF2"    "KHSRP"    "MRPS33"   "NDUFAF5"  "CDK5RAP1" "EARS2"   
##  [7] "MTFMT"    "SARS2"    "GTPBP10"  "DHX58"    "ATPAF1"   "NDUFAF4" 
## [13] "C6orf203" "MTO1"     "MRRF"     "MALSU1"   "MRPL55"   "NDUFS4"  
## [19] "PHAX"     "MRPL48"   "ZNF431"   "MRPL23"   "CCDC109B"
## $reactome
##                      category over_represented_pvalue under_represented_pvalue
## 495 mitochondrial translation            2.012426e-10                1.0000000
## 986               translation            1.162489e-06                0.9999999
##     numDEInCat numInCat          FDR
## 495          7        9 2.056700e-07
## 986          9       46 5.940318e-04
## 
## $go_bp
##                                 category over_represented_pvalue
## 1301       mitochondrial gene expression            0.000000e+00
## 1311           mitochondrial translation            0.000000e+00
## 1307 mitochondrial rna metabolic process            2.723763e-07
##      under_represented_pvalue numDEInCat numInCat          FDR
## 1301                        1         11       16 0.0000000000
## 1311                        1          9       13 0.0000000000
## 1307                        1          5        7 0.0003710674
## 
## [1] "set_2"
##  [1] "CENPQ"   "CENPO"   "ZNF816"  "RPS17"   "TNF"     "APBA2"   "RPL34"  
##  [8] "RPS12"   "RASGRF2" "EGR1"    "RPL21"   "FOSB"    "JUND"    "SORL1"  
## [15] "RPS27A"  "RPL9"    "RBKS"    "JUNB"    "RPLP2"   "RPS27"   "DNHD1"  
## [22] "RPS23"   "RPS18"  
## $reactome
##                                                        category
## 890 srp dependent cotranslational protein targeting to membrane
## 256                           eukaryotic translation initiation
## 734           response of eif2ak4 gcn2 to amino acid deficiency
## 255                           eukaryotic translation elongation
## 691                 regulation of expression of slits and robos
## 547                                 nonsense mediated decay nmd
## 808                                 selenoamino acid metabolism
## 117                             cellular response to starvation
## 869                                 signaling by robo receptors
## 387                                         influenza infection
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 890            1.367410e-08                        1         10       29
## 256            1.878780e-08                        1         10       30
## 734            1.912613e-08                        1         10       30
## 255            2.552031e-08                        1         10       31
## 691            2.648305e-08                        1         10       31
## 547            2.815049e-08                        1         10       31
## 808            3.633881e-08                        1         10       32
## 117            4.808493e-08                        1         10       33
## 869            4.815877e-08                        1         10       33
## 387            1.736204e-07                        1         10       37
##              FDR
## 890 4.794966e-06
## 256 4.794966e-06
## 734 4.794966e-06
## 255 4.794966e-06
## 691 4.794966e-06
## 547 4.794966e-06
## 808 5.305467e-06
## 117 5.468696e-06
## 869 5.468696e-06
## 387 1.774400e-05
## 
## $go_bp
##                       category over_represented_pvalue under_represented_pvalue
## 515    cytoplasmic translation            3.832737e-09                1.0000000
## 3637          response to salt            2.992022e-06                0.9999999
## 403  cellular response to salt            1.000833e-05                0.9999999
##      numDEInCat numInCat          FDR
## 515          10       33 0.0000156644
## 3637          5       11 0.0061141980
## 403           4        7 0.0136346749
## 
## $immune
##                                                          category
## 2358 gse26156 double positive vs cd4 single positive thymocyte up
## 1944                        gse22886 naive bcell vs neutrophil up
## 1974                                gse22886 naive tcell vs dc up
## 1940                                gse22886 naive bcell vs dc up
## 4064                    gse42088 uninf vs leishmania inf dc 2h dn
## 1725          gse21670 untreated vs tgfb il6 treated cd4 tcell dn
## 54                gaucher pbmc yf vax stamaril unknown age 7dy dn
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2358            6.228214e-07                1.0000000          8       36
## 1944            9.271724e-07                1.0000000          7       25
## 1974            7.059308e-06                0.9999996          7       33
## 1940            2.645149e-05                0.9999985          6       28
## 4064            3.236369e-05                0.9999980          6       29
## 1725            3.569177e-05                0.9999985          5       17
## 54              6.796412e-05                0.9999952          6       32
##              FDR
## 2358 0.002363826
## 1944 0.002363826
## 1974 0.011998471
## 1940 0.030332052
## 4064 0.030332052
## 1725 0.030332052
## 54   0.049507010
## 
## [1] "set_3"
##  [1] "MAD1L1"   "SLC25A14" "ERCC2"    "IMPDH1"   "C17orf75" "GTF2H3"  
##  [7] "CDC20"    "DCAF4"    "CKS2"     "MCEE"     "UROD"     "PDZD2"   
## [13] "CCNB1"    "CDK7"     "COPS3"    "CCNB2"    "MTHFD2L"  "POLE"    
## [19] "BTLA"     "HIST1H4J" "PRIM1"    "C1orf85"  "STK19"    "MUC20"   
## $reactome
##                                                    category
## 326         global genome nucleotide excision repair gg ner
## 967 transcription coupled nucleotide excision repair tc ner
## 574                              nucleotide excision repair
## 284                formation of tc ner pre incision complex
## 158 cyclin a b1 b2 associated events during g2 m transition
## 766               rna polymerase i transcription initiation
## 767              rna polymerase i transcription termination
## 283              formation of rna pol ii elongation complex
## 286               formation of the early elongation complex
## 370                            hiv transcription elongation
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 326            3.628575e-05                0.9999986          5       14
## 967            3.695727e-05                0.9999986          5       14
## 574            1.082683e-04                0.9999945          5       17
## 284            1.614574e-04                0.9999948          4       10
## 158            2.907588e-04                0.9999959          3        5
## 766            2.937602e-04                0.9999958          3        5
## 767            2.937602e-04                0.9999958          3        5
## 283            2.964478e-04                0.9999958          3        5
## 286            2.964478e-04                0.9999958          3        5
## 370            2.964478e-04                0.9999958          3        5
##            FDR
## 326 0.01888517
## 967 0.01888517
## 574 0.02754269
## 284 0.02754269
## 158 0.02754269
## 766 0.02754269
## 767 0.02754269
## 283 0.02754269
## 286 0.02754269
## 370 0.02754269
## 
## $go_bp
##                                 category over_represented_pvalue
## 1318 mitotic cell cycle phase transition            5.518124e-06
##      under_represented_pvalue numDEInCat numInCat        FDR
## 1318                0.9999996          8       42 0.02255257
## 
## [1] "set_18"
##  [1] "DUSP12"   "AAAS"     "DHPS"     "NUP107"   "GALE"     "NUP85"   
##  [7] "COQ3"     "FHOD1"    "ASNSD1"   "UCK2"     "LPP"      "CETN3"   
## [13] "VPS37A"   "GALK2"    "AGPAT6"   "NFU1"     "TMEM126A" "CTDNEP1" 
## [19] "UCKL1"    "ATP5J2"   "ABHD14A"  "GGT7"     "OBSCN"   
## $reactome
##                                                        category
## 562                                  nuclear envelope breakdown
## 400             interactions of rev with host cellular proteins
## 401             interactions of vpr with host cellular proteins
## 567                               nuclear import of rev protein
## 694 regulation of glucokinase by glucokinase regulatory protein
## 904                         sumoylation of sumoylation proteins
## 906                    sumoylation of ubiquitinylation proteins
## 257             export of viral ribonucleoproteins from nucleus
## 901                     sumoylation of dna replication proteins
## 903                         sumoylation of rna binding proteins
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 562            2.461663e-05                0.9999996          4        9
## 400            4.158902e-05                0.9999998          3        4
## 401            4.158902e-05                0.9999998          3        4
## 567            4.158902e-05                0.9999998          3        4
## 694            4.158902e-05                0.9999998          3        4
## 904            4.158902e-05                0.9999998          3        4
## 906            4.158902e-05                0.9999998          3        4
## 257            9.827123e-05                0.9999991          3        5
## 901            1.066252e-04                0.9999990          3        5
## 903            1.067353e-04                0.9999990          3        5
##             FDR
## 562 0.006071997
## 400 0.006071997
## 401 0.006071997
## 567 0.006071997
## 694 0.006071997
## 904 0.006071997
## 906 0.006071997
## 257 0.010005313
## 901 0.010005313
## 903 0.010005313
## 
## [1] "set_21"
##  [1] "ICA1"       "GBA2"       "REXO1"      "RABGGTA"    "ILVBL"     
##  [6] "SRM"        "PARP2"      "FGFBP2"     "MMS22L"     "SPON2"     
## [11] "COG5"       "XRCC6BP1"   "NT5DC1"     "HIST1H2BC"  "ZNF765"    
## [16] "HIST2H2AA4" "HIST2H2BF"  "TRAV14DV4"  "LINC00493"  "CNOT7P1"   
## [21] "HIST1H2BN"  "AC004069.2" "HIST1H3G"   "HNRNPA1P50" "FRMD4A"    
## $reactome
##                                                                                          category
## 356                                                                    hdacs deacetylate histones
## 355                                                                              hcmv late events
## 352                                                                       hats acetylate histones
## 353                                                                             hcmv early events
## 354                                                                                hcmv infection
## 10  activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 63                                       assembly of the orc complex at the origin of replication
## 122                         chromatin modifications during the maternal to zygotic transition mzt
## 209                                                                               dna methylation
## 249                                   ercc6 csb and ehmt2 g9a positively regulate rrna expression
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 356            1.991681e-05                0.9999995          5       11
## 355            5.548716e-05                0.9999980          5       15
## 352            7.931066e-05                0.9999968          5       16
## 353            9.596559e-05                0.9999959          5       17
## 354            1.234231e-04                0.9999944          5       18
## 10             2.169060e-04                0.9999935          4        9
## 63             2.169060e-04                0.9999935          4        9
## 122            2.169060e-04                0.9999935          4        9
## 209            2.169060e-04                0.9999935          4        9
## 249            2.169060e-04                0.9999935          4        9
##            FDR
## 356 0.01847316
## 355 0.01847316
## 352 0.01847316
## 353 0.01847316
## 354 0.01847316
## 10  0.01847316
## 63  0.01847316
## 122 0.01847316
## 209 0.01847316
## 249 0.01847316
## 
## [1] "set_29"
##  [1] "RNF10"     "SMG6"      "MICALL1"   "GMPR2"     "CNOT2"     "MTFR1L"   
##  [7] "APTX"      "CASP1"     "HAUS2"     "KSR1"      "MAP3K6"    "LIMD1"    
## [13] "C2orf44"   "DALRD3"    "PCGF5"     "CNOT10"    "EIF4ENIF1" "ZNF544"   
## [19] "TNRC6C"    "TNRC6B"    "CNOT6L"    "BTG2"      "PLA2G4B"  
## $reactome
##                                                                                                             category
## 952 tp53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
## 981                                                                               transcriptional regulation by tp53
## 954                                                                 tp53 regulates transcription of cell cycle genes
## 172                                                                                            deadenylation of mrna
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 952            3.560203e-06                1.0000000          4        6
## 981            7.267698e-06                0.9999996          7       35
## 954            1.346275e-05                0.9999998          4        8
## 172            6.478048e-05                0.9999996          3        4
##             FDR
## 952 0.003638527
## 981 0.003713794
## 954 0.004586311
## 172 0.016551413
## 
## $go_bp
##                                                                      category
## 1917                          nuclear transcribed mrna poly a tail shortening
## 1913 nuclear transcribed mrna catabolic process deadenylation dependent decay
## 1912                               nuclear transcribed mrna catabolic process
## 3702                                                      rna destabilization
## 2380                            positive regulation of mrna metabolic process
## 3201                                     regulation of mrna catabolic process
## 1372                                                   mrna catabolic process
## 1456                           negative regulation of amide metabolic process
## 3202                                     regulation of mrna metabolic process
## 3700                                                    rna catabolic process
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1917            3.599968e-11                1.0000000          7        8
## 1913            6.556969e-10                1.0000000          7       10
## 1912            9.780452e-10                1.0000000          8       15
## 3702            1.149893e-08                1.0000000          7       14
## 2380            4.080189e-08                1.0000000          7       16
## 3201            8.518372e-08                1.0000000          7       17
## 1372            9.073724e-08                1.0000000          8       24
## 1456            1.605856e-07                1.0000000          8       29
## 3202            4.392593e-07                1.0000000          7       21
## 3700            1.161380e-06                0.9999999          8       29
##               FDR
## 1917 1.471307e-07
## 1913 1.332424e-06
## 1912 1.332424e-06
## 3702 1.174903e-05
## 2380 3.335146e-05
## 3201 5.297759e-05
## 1372 5.297759e-05
## 1456 8.203918e-05
## 3202 1.994725e-04
## 3700 4.746562e-04
## 
## [1] "set_31"
##  [1] "Z97634.3"      "RASGRP2"       "TCF7"          "MAN1C1"       
##  [5] "ACVR2A"        "CCR7"          "C1orf162"      "PLAC8"        
##  [9] "LDLRAP1"       "PLXDC1"        "TMEM150A"      "CD248"        
## [13] "YPEL2"         "TRABD2A"       "MIR4461"       "CTD-3092A11.1"
## [17] "RP11-632K20.7" "LTB"           "CHRM3-AS2"     "WHAMMP2"      
## [21] "RP11-747H7.3"  "RP11-1000B6.3" "KCNQ1OT1"      "RP1-313I6.12" 
## [25] "RP11-434H6.7" 
## $immune
##                                                       category
## 3016                       gse32986 unstim vs gmcsf stim dc up
## 2390                    gse26495 naive vs pd1high cd8 tcell up
## 3005    gse32986 gmcsf vs gmcsf and curdlan lowdose stim dc dn
## 1702         gse21670 il6 vs tgfb and il6 treated cd4 tcell up
## 4341                 gse4984 lps vs vehicle ctrl treated dc up
## 3596              gse3982 basophil vs cent memory cd4 tcell dn
## 2392                     gse26495 naive vs pd1low cd8 tcell up
## 1799                                 gse22045 treg vs tconv dn
## 4400 gse5542 untreated vs ifna treated epithelial cells 24h dn
## 3391 gse37301 common lymphoid progenitor vs rag2 ko nk cell dn
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 3016            1.063057e-06                1.0000000          6       25
## 2390            3.744405e-06                0.9999999          6       30
## 3005            4.063936e-06                0.9999998          6       32
## 1702            5.818615e-06                0.9999998          5       22
## 4341            7.492212e-06                0.9999998          5       19
## 3596            1.233604e-05                0.9999998          4       10
## 2392            2.378461e-05                0.9999991          5       24
## 1799            7.385562e-05                0.9999978          4       15
## 4400            7.792784e-05                0.9999976          4       17
## 3391            8.332639e-05                0.9999975          4       15
##              FDR
## 3016 0.005420529
## 2390 0.006907337
## 3005 0.006907337
## 1702 0.007417279
## 4341 0.007640557
## 3596 0.010483582
## 2392 0.017325391
## 1799 0.042488128
## 4400 0.042488128
## 3391 0.042488128
## 
## [1] "set_37"
##  [1] "GCFC2"         "OAS1"          "GZMB"          "ENO3"         
##  [5] "NCOA7"         "GBP1"          "MT2A"          "RSAD2"        
##  [9] "SPPL2A"        "IRF8"          "SFR1"          "SLAMF8"       
## [13] "AMDHD2"        "GNGT2"         "KIR3DL1"       "ITGAM"        
## [17] "NINJ2"         "SWI5"          "PRF1"          "RP11-365H23.1"
## [21] "KIR2DS4"       "PTGES3P1"      "AKAP2"         "KIR2DL3"      
## [25] "SERHL2"       
## $immune
##                                            category over_represented_pvalue
## 55  gaucher pbmc yf vax stamaril unknown age 7dy up            2.244661e-07
## 45 gaucher pbmc yf vax stamaril unknown age 10dy up            1.517796e-05
##    under_represented_pvalue numDEInCat numInCat         FDR
## 55                 1.000000          9       45 0.001144553
## 45                 0.999999          7       39 0.038696207
## 
## [1] "set_39"
##  [1] "TNFSF10"      "PTGER2"       "IFI44L"       "IFI44"        "XCL1"        
##  [6] "XCL2"         "TRPT1"        "CX3CR1"       "MT1E"         "HOPX"        
## [11] "RP11-23P13.6" "ZNF683"       "NAP1L4P1"     "MTHFD2P7"     "EEF1GP1"     
## [16] "C10orf128"    "TRBV20-1"     "RP5-1053E7.3" "RP1-182O16.1" "RNU2-2P"     
## [21] "TSEN15P1"     "SNRPEP4"      "MIR155HG"     "RNU1-125P"    "AL358333.1"  
## $reactome
##                               category over_represented_pvalue
## 127 class a 1 rhodopsin like receptors            1.176486e-05
## 349                gpcr ligand binding            2.673622e-05
##     under_represented_pvalue numDEInCat numInCat        FDR
## 127                0.9999999          4       19 0.01202368
## 349                0.9999996          4       23 0.01366221
saveRDS(goseq_res, sprintf("output/gene_set_enrichments_%s.RDS", 
                           file_tag))

Session information

gc()
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8958520 478.5   17165476 916.8         NA 17165476 916.8
## Vcells 19169159 146.3   59533611 454.3      65536 78485130 598.8
sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
##  [2] GenomicFeatures_1.50.4                  
##  [3] GenomicRanges_1.50.2                    
##  [4] GenomeInfoDb_1.34.9                     
##  [5] org.Hs.eg.db_3.16.0                     
##  [6] AnnotationDbi_1.60.2                    
##  [7] IRanges_2.32.0                          
##  [8] S4Vectors_0.36.2                        
##  [9] Biobase_2.58.0                          
## [10] BiocGenerics_0.44.0                     
## [11] goseq_1.50.0                            
## [12] geneLenDataBase_1.34.0                  
## [13] BiasedUrn_2.0.10                        
## [14] fgsea_1.24.0                            
## [15] biomaRt_2.54.1                          
## [16] limma_3.54.2                            
## [17] tidyr_1.3.0                             
## [18] ggpubr_0.6.0                            
## [19] ggplot2_3.4.2                           
## [20] data.table_1.14.8                       
## 
## loaded via a namespace (and not attached):
##  [1] nlme_3.1-162                matrixStats_1.0.0          
##  [3] bitops_1.0-7                bit64_4.0.5                
##  [5] filelock_1.0.2              progress_1.2.2             
##  [7] httr_1.4.6                  tools_4.2.3                
##  [9] backports_1.4.1             bslib_0.4.2                
## [11] utf8_1.2.3                  R6_2.5.1                   
## [13] mgcv_1.8-42                 DBI_1.1.3                  
## [15] colorspace_2.1-0            withr_2.5.0                
## [17] tidyselect_1.2.0            prettyunits_1.1.1          
## [19] bit_4.0.5                   curl_5.0.1                 
## [21] compiler_4.2.3              cli_3.6.1                  
## [23] xml2_1.3.4                  DelayedArray_0.24.0        
## [25] rtracklayer_1.58.0          sass_0.4.5                 
## [27] scales_1.2.1                rappdirs_0.3.3             
## [29] Rsamtools_2.14.0            stringr_1.5.0              
## [31] digest_0.6.31               rmarkdown_2.21             
## [33] XVector_0.38.0              pkgconfig_2.0.3            
## [35] htmltools_0.5.5             MatrixGenerics_1.10.0      
## [37] dbplyr_2.3.2                fastmap_1.1.1              
## [39] rlang_1.1.0                 rstudioapi_0.14            
## [41] RSQLite_2.3.1               BiocIO_1.8.0               
## [43] jquerylib_0.1.4             generics_0.1.3             
## [45] jsonlite_1.8.4              BiocParallel_1.32.6        
## [47] dplyr_1.1.2                 car_3.1-2                  
## [49] RCurl_1.98-1.12             magrittr_2.0.3             
## [51] GO.db_3.16.0                GenomeInfoDbData_1.2.9     
## [53] Matrix_1.6-4                Rcpp_1.0.10                
## [55] munsell_0.5.0               fansi_1.0.4                
## [57] abind_1.4-5                 lifecycle_1.0.3            
## [59] stringi_1.7.12              yaml_2.3.7                 
## [61] carData_3.0-5               SummarizedExperiment_1.28.0
## [63] zlibbioc_1.44.0             BiocFileCache_2.6.1        
## [65] grid_4.2.3                  blob_1.2.4                 
## [67] parallel_4.2.3              crayon_1.5.2               
## [69] lattice_0.20-45             splines_4.2.3              
## [71] Biostrings_2.66.0           cowplot_1.1.1              
## [73] hms_1.1.3                   KEGGREST_1.38.0            
## [75] knitr_1.44                  pillar_1.9.0               
## [77] rjson_0.2.21                ggsignif_0.6.4             
## [79] codetools_0.2-19            fastmatch_1.1-3            
## [81] XML_3.99-0.14               glue_1.6.2                 
## [83] evaluate_0.20               png_0.1-8                  
## [85] vctrs_0.6.2                 gtable_0.3.3               
## [87] purrr_1.0.1                 cachem_1.0.7               
## [89] xfun_0.39                   broom_1.0.4                
## [91] restfulr_0.0.15             rstatix_0.7.2              
## [93] tibble_3.2.1                GenomicAlignments_1.34.1   
## [95] memoise_2.0.1